Starting phenix.real_space_refine on Sun Dec 29 01:54:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j91_36084/12_2024/8j91_36084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j91_36084/12_2024/8j91_36084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j91_36084/12_2024/8j91_36084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j91_36084/12_2024/8j91_36084.map" model { file = "/net/cci-nas-00/data/ceres_data/8j91_36084/12_2024/8j91_36084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j91_36084/12_2024/8j91_36084.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 226 5.49 5 S 10 5.16 5 C 5557 2.51 5 N 1843 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9944 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 598 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 665 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 688 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 694 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2301 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "J" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2332 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Time building chain proxies: 6.11, per 1000 atoms: 0.61 Number of scatterers: 9944 At special positions: 0 Unit cell: (119.78, 118.72, 101.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 226 15.00 O 2308 8.00 N 1843 7.00 C 5557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 726.7 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 75.2% alpha, 2.9% beta 79 base pairs and 200 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.868A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.605A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.894A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.537A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.776A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 57 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.538A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.724A pdb=" N GLN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 108 removed outlier: 3.649A pdb=" N LEU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 128 through 149 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.676A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.902A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.656A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 removed outlier: 3.539A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 48 through 74 removed outlier: 3.893A pdb=" N ALA G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 removed outlier: 3.778A pdb=" N ILE G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 85 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 128 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.075A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.468A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.788A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.073A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.291A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 367 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 396 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 200 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 4 1.21 - 1.36: 2977 1.36 - 1.51: 4403 1.51 - 1.66: 3171 1.66 - 1.81: 18 Bond restraints: 10573 Sorted by residual: bond pdb=" C6 DG I -52 " pdb=" O6 DG I -52 " ideal model delta sigma weight residual 1.239 1.065 0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C4 DC J 52 " pdb=" N4 DC J 52 " ideal model delta sigma weight residual 1.337 1.187 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C1' DA I 24 " pdb=" N9 DA I 24 " ideal model delta sigma weight residual 1.460 1.363 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" CA ALA E 96 " pdb=" CB ALA E 96 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.59e-02 3.96e+03 1.72e+01 bond pdb=" O3' DC J 24 " pdb=" P DT J 25 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.66e+01 ... (remaining 10568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 15191 6.26 - 12.53: 43 12.53 - 18.79: 3 18.79 - 25.05: 1 25.05 - 31.31: 4 Bond angle restraints: 15242 Sorted by residual: angle pdb=" O3' DA I 24 " pdb=" P DG I 25 " pdb=" O5' DG I 25 " ideal model delta sigma weight residual 104.00 131.03 -27.03 1.50e+00 4.44e-01 3.25e+02 angle pdb=" O3' DA I 24 " pdb=" P DG I 25 " pdb=" OP2 DG I 25 " ideal model delta sigma weight residual 108.00 76.69 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb=" OP2 DG I 25 " pdb=" P DG I 25 " pdb=" O5' DG I 25 " ideal model delta sigma weight residual 108.00 78.64 29.36 3.00e+00 1.11e-01 9.58e+01 angle pdb=" O3' DC J 24 " pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 111.50 96.95 14.55 1.50e+00 4.44e-01 9.41e+01 angle pdb=" O3' DT J 54 " pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 111.50 125.27 -13.77 1.50e+00 4.44e-01 8.42e+01 ... (remaining 15237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 4661 32.97 - 65.95: 1057 65.95 - 98.92: 34 98.92 - 131.89: 2 131.89 - 164.86: 2 Dihedral angle restraints: 5756 sinusoidal: 3800 harmonic: 1956 Sorted by residual: dihedral pdb=" C4' DA I 24 " pdb=" C3' DA I 24 " pdb=" O3' DA I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 55.14 164.86 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 58.65 161.35 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA ASP C 100 " pdb=" CB ASP C 100 " pdb=" CG ASP C 100 " pdb=" OD1 ASP C 100 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 5753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1652 0.128 - 0.257: 84 0.257 - 0.385: 9 0.385 - 0.514: 3 0.514 - 0.642: 1 Chirality restraints: 1749 Sorted by residual: chirality pdb=" C3' DA I 24 " pdb=" C4' DA I 24 " pdb=" O3' DA I 24 " pdb=" C2' DA I 24 " both_signs ideal model delta sigma weight residual False -2.66 -3.30 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DT J 25 " pdb=" OP1 DT J 25 " pdb=" OP2 DT J 25 " pdb=" O5' DT J 25 " both_signs ideal model delta sigma weight residual True 2.35 -1.86 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 1746 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 57 " -0.174 2.00e-02 2.50e+03 9.24e-02 2.56e+02 pdb=" N9 DG J 57 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DG J 57 " 0.163 2.00e-02 2.50e+03 pdb=" N7 DG J 57 " 0.123 2.00e-02 2.50e+03 pdb=" C5 DG J 57 " -0.034 2.00e-02 2.50e+03 pdb=" C6 DG J 57 " -0.072 2.00e-02 2.50e+03 pdb=" O6 DG J 57 " -0.107 2.00e-02 2.50e+03 pdb=" N1 DG J 57 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DG J 57 " 0.031 2.00e-02 2.50e+03 pdb=" N2 DG J 57 " 0.101 2.00e-02 2.50e+03 pdb=" N3 DG J 57 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DG J 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -5 " -0.211 2.00e-02 2.50e+03 9.46e-02 2.46e+02 pdb=" N9 DA I -5 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DA I -5 " 0.102 2.00e-02 2.50e+03 pdb=" N7 DA I -5 " 0.092 2.00e-02 2.50e+03 pdb=" C5 DA I -5 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA I -5 " -0.051 2.00e-02 2.50e+03 pdb=" N6 DA I -5 " -0.143 2.00e-02 2.50e+03 pdb=" N1 DA I -5 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -5 " 0.081 2.00e-02 2.50e+03 pdb=" N3 DA I -5 " 0.060 2.00e-02 2.50e+03 pdb=" C4 DA I -5 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -21 " -0.144 2.00e-02 2.50e+03 8.09e-02 1.96e+02 pdb=" N9 DG J -21 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG J -21 " 0.136 2.00e-02 2.50e+03 pdb=" N7 DG J -21 " 0.119 2.00e-02 2.50e+03 pdb=" C5 DG J -21 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DG J -21 " -0.060 2.00e-02 2.50e+03 pdb=" O6 DG J -21 " -0.095 2.00e-02 2.50e+03 pdb=" N1 DG J -21 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DG J -21 " 0.035 2.00e-02 2.50e+03 pdb=" N2 DG J -21 " 0.095 2.00e-02 2.50e+03 pdb=" N3 DG J -21 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG J -21 " -0.021 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 225 2.68 - 3.23: 8262 3.23 - 3.79: 17170 3.79 - 4.34: 23603 4.34 - 4.90: 34329 Nonbonded interactions: 83589 Sorted by model distance: nonbonded pdb=" C2' DA I 24 " pdb=" OP1 DG I 25 " model vdw 2.122 3.440 nonbonded pdb=" C4' DA I 24 " pdb=" OP1 DG I 25 " model vdw 2.163 3.470 nonbonded pdb=" O LEU G 86 " pdb=" ND2 ASN G 90 " model vdw 2.205 3.120 nonbonded pdb=" C3' DA I 24 " pdb=" OP1 DG I 25 " model vdw 2.229 2.776 nonbonded pdb=" NZ LYS G 36 " pdb=" OP2 DA I 39 " model vdw 2.297 3.120 ... (remaining 83584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 61 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 106) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.890 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.174 10573 Z= 0.562 Angle : 1.552 31.314 15242 Z= 0.964 Chirality : 0.069 0.642 1749 Planarity : 0.015 0.095 1143 Dihedral : 26.616 164.864 4492 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.31), residues: 662 helix: 1.58 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE G 26 TYR 0.017 0.002 TYR D 65 ARG 0.006 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7852 (mmtm) REVERT: D 84 MET cc_start: 0.7773 (mmp) cc_final: 0.7542 (mmt) REVERT: H 110 LYS cc_start: 0.8022 (mppt) cc_final: 0.7799 (mmtp) REVERT: H 141 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8140 (ttmm) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 2.0345 time to fit residues: 285.1361 Evaluate side-chains 77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS B 27 GLN C 74 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN G 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10573 Z= 0.214 Angle : 0.777 37.825 15242 Z= 0.392 Chirality : 0.039 0.585 1749 Planarity : 0.005 0.046 1143 Dihedral : 30.382 161.266 3192 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.80 % Allowed : 10.23 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.32), residues: 662 helix: 2.12 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.008 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.798 Fit side-chains REVERT: A 129 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7698 (ttt90) REVERT: B 79 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7836 (mmtm) REVERT: C 36 LYS cc_start: 0.8019 (mttt) cc_final: 0.7629 (mttp) REVERT: C 73 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6526 (t0) REVERT: C 89 ARG cc_start: 0.6805 (mmt90) cc_final: 0.6558 (mmt90) REVERT: H 65 TYR cc_start: 0.8634 (m-80) cc_final: 0.8238 (m-80) REVERT: H 93 ASP cc_start: 0.7852 (t70) cc_final: 0.7366 (t70) outliers start: 10 outliers final: 2 residues processed: 101 average time/residue: 1.6633 time to fit residues: 177.2019 Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN F 25 ASN F 93 GLN G 74 ASN G 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10573 Z= 0.323 Angle : 0.628 10.587 15242 Z= 0.362 Chirality : 0.038 0.156 1749 Planarity : 0.005 0.045 1143 Dihedral : 30.743 170.209 3192 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.59 % Allowed : 10.77 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.32), residues: 662 helix: 1.90 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.45 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.011 0.002 PHE A 104 TYR 0.020 0.002 TYR F 51 ARG 0.007 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.789 Fit side-chains REVERT: A 76 GLN cc_start: 0.7625 (tt0) cc_final: 0.7302 (pt0) REVERT: B 63 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 79 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7895 (mmtp) REVERT: C 36 LYS cc_start: 0.7980 (mttt) cc_final: 0.7530 (mttp) REVERT: C 73 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6492 (t0) REVERT: C 89 ARG cc_start: 0.6947 (mmt90) cc_final: 0.6674 (mmt90) REVERT: C 103 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8339 (mm) REVERT: D 147 THR cc_start: 0.7949 (m) cc_final: 0.7656 (m) REVERT: G 80 VAL cc_start: 0.8642 (m) cc_final: 0.8421 (m) REVERT: H 65 TYR cc_start: 0.8662 (m-80) cc_final: 0.8393 (m-80) REVERT: H 93 ASP cc_start: 0.8070 (t70) cc_final: 0.7687 (t70) REVERT: H 138 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7684 (mm-30) outliers start: 20 outliers final: 8 residues processed: 107 average time/residue: 1.8181 time to fit residues: 204.4285 Evaluate side-chains 100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10573 Z= 0.200 Angle : 0.569 9.719 15242 Z= 0.338 Chirality : 0.035 0.149 1749 Planarity : 0.005 0.049 1143 Dihedral : 30.678 163.923 3192 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.51 % Allowed : 13.82 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.32), residues: 662 helix: 2.17 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.40 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7591 (tt0) cc_final: 0.7268 (pt0) REVERT: B 63 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 79 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7839 (mmtp) REVERT: C 36 LYS cc_start: 0.7983 (mttt) cc_final: 0.7540 (mttp) REVERT: C 73 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6514 (t0) REVERT: C 103 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8314 (mm) REVERT: D 147 THR cc_start: 0.7982 (m) cc_final: 0.7707 (m) REVERT: E 122 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7791 (ptmt) REVERT: G 78 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7160 (ttt180) REVERT: G 80 VAL cc_start: 0.8613 (m) cc_final: 0.8384 (m) REVERT: H 65 TYR cc_start: 0.8620 (m-80) cc_final: 0.8320 (m-80) REVERT: H 93 ASP cc_start: 0.7989 (t70) cc_final: 0.7586 (t70) outliers start: 14 outliers final: 6 residues processed: 99 average time/residue: 1.7893 time to fit residues: 186.2749 Evaluate side-chains 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10573 Z= 0.330 Angle : 0.620 10.599 15242 Z= 0.359 Chirality : 0.038 0.158 1749 Planarity : 0.006 0.058 1143 Dihedral : 30.820 162.180 3192 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.05 % Allowed : 14.36 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.31), residues: 662 helix: 2.00 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.010 0.002 PHE A 104 TYR 0.018 0.002 TYR F 51 ARG 0.006 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7635 (tt0) cc_final: 0.7273 (pt0) REVERT: B 63 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7610 (mt-10) REVERT: B 79 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7839 (mmtp) REVERT: C 36 LYS cc_start: 0.7918 (mttt) cc_final: 0.7481 (mttp) REVERT: C 73 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6616 (t0) REVERT: C 82 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7175 (ttp80) REVERT: C 103 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8403 (mm) REVERT: D 108 TYR cc_start: 0.7115 (m-10) cc_final: 0.6819 (t80) REVERT: H 65 TYR cc_start: 0.8652 (m-80) cc_final: 0.8362 (m-80) REVERT: H 141 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7974 (ttpp) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 1.9280 time to fit residues: 210.4459 Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10573 Z= 0.272 Angle : 0.587 10.016 15242 Z= 0.345 Chirality : 0.037 0.166 1749 Planarity : 0.005 0.055 1143 Dihedral : 30.782 162.281 3192 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.87 % Allowed : 16.34 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.31), residues: 662 helix: 2.10 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.53 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.009 0.002 PHE E 67 TYR 0.016 0.002 TYR F 51 ARG 0.008 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7626 (tt0) cc_final: 0.7285 (pt0) REVERT: B 63 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7610 (mt-10) REVERT: B 79 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7835 (mmtp) REVERT: C 36 LYS cc_start: 0.7928 (mttt) cc_final: 0.7495 (mttp) REVERT: C 73 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6613 (t0) REVERT: C 82 ARG cc_start: 0.7476 (ttp80) cc_final: 0.7169 (ttp80) REVERT: D 108 TYR cc_start: 0.7120 (m-10) cc_final: 0.6815 (t80) REVERT: H 65 TYR cc_start: 0.8637 (m-80) cc_final: 0.8389 (m-80) REVERT: H 93 ASP cc_start: 0.8075 (t70) cc_final: 0.7691 (t70) REVERT: H 141 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8000 (ttpt) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 1.8225 time to fit residues: 188.9174 Evaluate side-chains 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10573 Z= 0.201 Angle : 0.565 9.712 15242 Z= 0.336 Chirality : 0.035 0.234 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.769 162.128 3192 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.41 % Allowed : 15.98 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.32), residues: 662 helix: 2.28 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.45 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7609 (tt0) cc_final: 0.7276 (pt0) REVERT: B 63 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 79 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7814 (mmtp) REVERT: C 36 LYS cc_start: 0.7916 (mttt) cc_final: 0.7498 (mttp) REVERT: C 73 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6618 (t0) REVERT: C 82 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7149 (ttp80) REVERT: D 108 TYR cc_start: 0.7064 (m-10) cc_final: 0.6786 (t80) REVERT: H 65 TYR cc_start: 0.8621 (m-80) cc_final: 0.8353 (m-80) REVERT: H 93 ASP cc_start: 0.8012 (t70) cc_final: 0.7589 (t70) REVERT: H 141 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8030 (ttpt) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 1.8004 time to fit residues: 183.4811 Evaluate side-chains 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10573 Z= 0.327 Angle : 0.610 10.260 15242 Z= 0.355 Chirality : 0.038 0.206 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.862 162.176 3192 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.87 % Allowed : 16.70 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.31), residues: 662 helix: 2.11 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.58 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.009 0.002 PHE E 67 TYR 0.016 0.002 TYR F 51 ARG 0.007 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7670 (tt0) cc_final: 0.7285 (pt0) REVERT: B 63 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 79 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7777 (mmtp) REVERT: C 25 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7368 (mp10) REVERT: C 36 LYS cc_start: 0.7923 (mttt) cc_final: 0.7496 (mttp) REVERT: C 73 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6628 (t0) REVERT: C 82 ARG cc_start: 0.7441 (ttp80) cc_final: 0.6993 (tpt170) REVERT: D 108 TYR cc_start: 0.7169 (m-10) cc_final: 0.6852 (t80) REVERT: G 57 GLU cc_start: 0.8010 (tt0) cc_final: 0.7665 (tt0) REVERT: H 65 TYR cc_start: 0.8662 (m-80) cc_final: 0.8421 (m-80) REVERT: H 93 ASP cc_start: 0.8138 (t70) cc_final: 0.7920 (t70) REVERT: H 141 LYS cc_start: 0.8391 (ttmm) cc_final: 0.7984 (ttpp) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 1.8883 time to fit residues: 188.3081 Evaluate side-chains 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10573 Z= 0.211 Angle : 0.578 9.734 15242 Z= 0.342 Chirality : 0.036 0.214 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.842 161.864 3192 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.97 % Allowed : 17.24 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.32), residues: 662 helix: 2.31 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.51 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.005 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7659 (tt0) cc_final: 0.7308 (pt0) REVERT: B 63 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7595 (mt-10) REVERT: B 79 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7765 (mmtp) REVERT: C 25 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7361 (mp10) REVERT: C 36 LYS cc_start: 0.7925 (mttt) cc_final: 0.7496 (mttp) REVERT: C 73 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6526 (t0) REVERT: C 82 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7055 (tpt170) REVERT: D 108 TYR cc_start: 0.7132 (m-10) cc_final: 0.6779 (t80) REVERT: H 65 TYR cc_start: 0.8627 (m-80) cc_final: 0.8389 (m-80) REVERT: H 93 ASP cc_start: 0.8089 (t70) cc_final: 0.7710 (t70) REVERT: H 141 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7989 (ttpt) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 1.9357 time to fit residues: 180.8526 Evaluate side-chains 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 10573 Z= 0.481 Angle : 0.699 10.792 15242 Z= 0.400 Chirality : 0.044 0.154 1749 Planarity : 0.007 0.082 1143 Dihedral : 31.169 162.474 3192 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.80 % Allowed : 17.95 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 662 helix: 1.75 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -0.82 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.011 0.003 PHE E 67 TYR 0.013 0.003 TYR C 40 ARG 0.008 0.001 ARG E 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7677 (tt0) cc_final: 0.7327 (pt0) REVERT: B 63 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 79 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7804 (mmtp) REVERT: C 25 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7417 (mp10) REVERT: C 36 LYS cc_start: 0.7933 (mttt) cc_final: 0.7514 (mttp) REVERT: C 73 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6461 (t0) REVERT: C 82 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7004 (tpt170) REVERT: D 108 TYR cc_start: 0.7196 (m-10) cc_final: 0.6744 (t80) REVERT: G 57 GLU cc_start: 0.8073 (tt0) cc_final: 0.7734 (tt0) REVERT: H 63 LYS cc_start: 0.8317 (mptt) cc_final: 0.7204 (ttpp) REVERT: H 65 TYR cc_start: 0.8686 (m-80) cc_final: 0.8392 (m-80) REVERT: H 141 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7913 (ttpm) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 1.8387 time to fit residues: 181.6421 Evaluate side-chains 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN H 72 GLN H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.175593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126460 restraints weight = 10434.916| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.23 r_work: 0.3083 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10573 Z= 0.200 Angle : 0.590 9.297 15242 Z= 0.352 Chirality : 0.037 0.136 1749 Planarity : 0.005 0.056 1143 Dihedral : 30.999 162.324 3192 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.08 % Allowed : 19.57 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.32), residues: 662 helix: 2.26 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.62 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.015 0.002 TYR D 62 ARG 0.007 0.001 ARG C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.96 seconds wall clock time: 59 minutes 52.54 seconds (3592.54 seconds total)